I am already in side Bowser. I'm controlling him right now on his way to his first fight. The game then crashes as the fight starts.
To solve the first fight freezing (metaboss or Bowser Boss Battle), I disabled the audio in a scene *before* the scene when battle starts (ie. when you see some ships destroying the Bowser castle) or even before, depending how much of the game you want to play without audio. If you disable it just before the battle starts, won't work (or at least didn't work for me).
Anyway, when the battle starts (and with the audio off), you will see a black screen on the upper screen and a white on the lower instead the graphic corruption and later crash. Just turn on the audio again (mono or stereo) and the battle should start fine.
I guess is an audio related bug, don't ask me why it crashes like that.
The other thing is converting the No$GBA save to RAW format (Autodetection) using a save converter (like ShunyWeb).... use desmume with that save and get past that battle, then use No$GBA again if you want. The problem with desmume is that... it is overall slower with this game, even using the latest SVN.